Aptamers: molecular tools for analytical applications

Aptamers are artificial nucleic acid ligands, specifically generated against certain targets, such as amino acids, drugs, proteins or other molecules. In nature they exist as a nucleic acid based genetic regulatory element called a riboswitch. For generation of artificial ligands, they are isolated from combinatorial libraries of synthetic nucleic acid by exponential enrichment, via an in vitro iterative process of adsorption, recovery and reamplification known as systematic evolution of ligands by exponential enrichment (SELEX). Thanks to their unique characteristics and chemical structure, aptamers offer themselves as ideal candidates for use in analytical devices and techniques. Recent progress in the aptamer selection and incorporation of aptamers into molecular beacon structures will ensure the application of aptamers for functional and quantitative proteomics and high-throughput screening for drug discovery, as well as in various analytical applications. The properties of aptamers as well as recent developments in improved, time-efficient methods for their selection and stabilization are outlined. The use of these powerful molecular tools for analysis and the advantages they offer over existing affinity biocomponents are discussed. Finally the evolving use of aptamers in specific analytical applications such as chromatography, ELISA-type assays, biosensors and affinity PCR as well as current avenues of research and future perspectives conclude this review.     

Photoresponsive molecular switches for biotechnology

The use of light to control chemical and biological systems with the advantages of high speed and spatiotemporal precision offers many intriguing possibilities. The field of photoresponsive molecular switches for biotechnology is emerging as a fascinating area of research for their great potential in biomedical applications as smart triggers. Here recent development of photoresponsive molecular switches for biotechnology is reviewed, where the fabrication, physicochemical properties and applications in biotechnology are highlighted, especially focused on controlling the immobilization of biomolecules on surfaces and the conformation of biomolecules by the photoswitches.     

Acetylenic cyclophanes: emerging carbon-rich compounds for molecular construction and practical applications

The preparation of simple acetylenic [2.2]parcyclophane ‘building blocks’ is described. These compounds are readily available from the commercially available [2.2]paracyclophane employing functionalization of the parent system and conversion of the resulting functional groups into triple bonds. For the incorporation of these structures into cyclophanes with ‘extended’ π-systems, coupling reactions such as the Sonogashira or the Glaser coupling are particularly valuable. Besides addition reactions the ethynyl cyclophanes can be employed to prepare novel iron, platinum, and cobalt metal complexes. By polycondensation reactions the monomeric cyclophanes can be converted into novel polymers displaying lateral π-conjugation. The application of alkynylcyclophanes in material science and nanochemistry is discussed.     

Proteomics in molecular medicine: applications in central nervous systems disorders

Bodily fluids such as cerebrospinal fluid (CSF) and serum can be analysed at the time of presentation and throughout the course of the disease. Changes in the protein composition of CSF may be indicative of altered CNS protein expression pattern with a causative or diagnostic disease link. These findings can be strengthened through subsequent proteomic analysis of specific brain areas implicated in the pathology. New isolation strategies of clinically relevant cellular material such as laser capture microdissection, protein enrichment procedures and proteomic approaches to neuropeptide and neurotransmitter analysis give us the opportunity to map out complex cellular interaction at an unprecedented level of detail. In neurological disorders multiple underlying pathogenic mechanisms as well as an acute and a chronic CNS disease components may require a selective repertoire of molecular targets and biomarkers rather than an individual protein to better define a complex disease. The resulting proteome database bypasses many ambiguities of experimental models and may facilitate pre- and clinical development of more specific disease markers and new selective fast acting therapeutics.     

Portable tools and applications for parallel computers

A distributed-memory model is adopted for the development of parallel ab initio codes with an emphasis on portability as well as efficiency. A highly portable message-passing toolkit (inspired by the Argonne ACRF PARMACS ) is described. Examples and results of its use are presented.     

Photoresponsive molecular recognition and adhesion of vesicles in a competitive ternary supramolecular system

A competitive photoresponsive supramolecular system is formed in a dilute aqueous solution of three components: vesicles of amphiphilic α-cyclodextrin host 1a, divalent p-methylphenyl guest 2 or divalent p-methylbenzamide guest 3, and photoresponsive azobenzene monovalent guest 5. Guests 2 and 3 form weak inclusion complexes with 1a (K(a)≈10(2) M(-1)), whereas azobenzene guest 5 forms a strong inclusion complex (K(a)≈10(4) M(-1)), provided it is in the trans state. The aggregation and adhesion of vesicles of host 1a is mediated by guest 2 (or 3) due to the formation of multiple intervesicular noncovalent links, as confirmed by using isothermal titration calorimetry (ITC), optical density measurements at 600 nm (OD600), dynamic light scattering (DLS), and cryogenic transmission electron microscopy (cryo-TEM). The addition of excess monovalent guest trans-5 to vesicles of 1a aggregated by divalent guest 2 (or 3) causes the dispersion of vesicles of 1a because trans-5 displaces 2 (as well as 3) from the vesicle surface. Upon UV irradiation of a dilute ternary mixture of vesicles of 1a, guest 2 (or 3), and competitor trans-5, compound trans-5 isomerizes to cis-5, and renewed aggregation of vesicles of 1a by guest 2 (or 3) occurs because 2 (as well as 3) displaces cis-5 from the vesicle surface. Subsequent visible irradiation causes the redispersion of vesicles of 1a because cis-5 reisomerizes into trans-5, which again displaces guest 2 (or 3) from the vesicle surface. In this way, the competitive photoresponsive aggregation and dispersion of vesicles can be repeated for several cycles.     

Tailored jeffamine molecular tools for ordering mesoporous silica

Herein, we report the formation of organized mesoporous silica materials prepared from a novel nonionic gemini surfactant, myristoyl-end-capped Jeffamine, synthesized from a polyoxyalkyleneamine (ED900). The behavior of the modified Jeffamine in water was first investigated. A direct micellar phase (L(1)) and a hexagonal (H(1)) liquid crystal were found. The structure of the micelles was investigated from the SAXS and the analysis by generalized indirect Fourier transformation, which show that the particles are globular of core-shell type. The myristoyl chains, located at the ends of the amphiphile molecule, are assembled to form the core of the micelles and, as a consequence, the molecules are folded over on themselves. Mesoporous materials were then synthesized from the self-assembly mechanism. The recovered materials were characterized by SAXS measurements, nitrogen adsorption-desorption analysis, and transmission and scanning electron microscopy. The results clearly evidence that by modifying the synthesis parameters, such as the surfactant/silica precursor molar ratio and the hydrothermal conditions, one can control the size and the nanostructuring of the resulting material. It was observed that, the lower the temperature of the hydrothermal treatment, the better the mesopore ordering.     

High-density synthetic peptide microarrays: emerging tools for functional genomics and proteomics

New approaches for manufacturing and application of peptide arrays on planar surfaces are emerging, thereby opening advanced opportunities to probe the expression and function of the proteome. In complementing DNA and protein array analyses, peptide fragment screening directly addresses functional protein interaction sites, leading to a detailed insight into the discovered molecular recognition events, placing them in the context of the whole genome, and even allowing rapid determination of the chemical nature of these interactions. This information can then be transferred into powerful small peptide tools that interfere with these interactions in vivo and help to link targets with phenotypes. With the spreading of new peptide array tools, peptide screening will extend its impact on modern genome-driven molecular biology. This will advance the systematic discovery and validation of new pharmaceutical targets as well as the development of potent molecular diagnostics for medical and ecological monitoring.     

Photoresponsive molecular wires of FeII triazole complexes in organic media and light-induced morphological transformations

A lipophilic linear FeII 1,2,4-triazole complex containing azobenzene chromophores forms molecular wires in organic solvents; photoisomerization of azobenzene units induced morphological changes that lead to reversible, macroscopic gel-to-sol transition phenomena.     

Cruciform pi-systems for molecular electronics applications

This study details a modular and general synthesis of a new class of molecules consisting of cruciform pi-systems. The key to synthesizing these molecules was an unprecedented double Staudinger cyclization. Once formed, these rigid compounds assemble into ordered monolayer films on metal and metal oxide surfaces to orient their conjugated, bis-phenyloxazole subunits upright. This surface orientation is enforced by the external phenyl substituents that are out of the ring plane, thus preventing the prone conformation.     

Gaussian basis sets for molecular applications

The choice of basis set in quantum chemical calculations can have a huge impact on the quality of the results, especially for correlated ab initio methods. This article provides an overview of the development of Gaussian basis sets for molecular calculations, with a focus on four popular families of modern atom‐centered, energy‐optimized bases: atomic natural orbital, correlation consistent, polarization consistent, and def2. The terminology used for describing basis sets is briefly covered, along with an overview of the auxiliary basis sets used in a number of integral approximation techniques and an outlook on possible future directions of basis set design. © 2012 Wiley Periodicals, Inc.     

The emerging applications of pillararene architectures in supramolecular catalysis

Over the last decade, numerous research efforts have been devoted to pillar[n]arenes since their debut.The popularity of pillararenes is a reflection of current research trend in supramolecular and macrocyclic chemistry in general. Among the vast applications(such as chemosensors, drug delivery, transmembrance channels, and separation) of pillararenes, their utilization in catalysis is a relatively less explored area.However, soaring attention has been paid by researchers in recent years and thi...     

Miniaturized tools and devices for bioanalytical applications: an overview

This article presents an overview of various miniaturized devices and technologies developed by our group. Innovative, fast and cheap procedures for the fabrication of laboratory microsystems based on commercially available materials are reported and compared with well-established microfabrication techniques. The modules fabricated and tested in our laboratory can be used independently or they can be set up in different configurations to form functional measurement systems. We also report further applications of the presented modules e.g. disposable poly(dimethylsiloxane) (PDMS) microcuvettes, fibre optic detectors, potentiometric sensors platforms, microreactors and capillary electrophoresis (CE) microchips as well as integrated microsystems e.g. double detection microanalytical systems, devices for studying enzymatic reactions and a microsystem for cell culture and lysis.     

Lectins: tools for the molecular understanding of the glycocode

Recent progress in glycobiology has revealed that cell surface oligosaccharides play an essential role in recognition events. More precisely, these saccharides may be complexed by lectins, carbohydrate-binding proteins other than enzymes and antibodies, able to recognise sugars in a highly specific manner. The ubiquity of lectin-carbohydrate interactions opens enormous potential for their exploitation in medicine. Therefore, extraordinary effort is made into the identification of new lectins as well as into the achievement of a deep understanding of their functions and of the precise mechanism of their association with specific ligands. In this review, a summary of the main features of lectins, particularly those found in legumes, will be presented with a focus on the mechanism of carbohydrate-binding. An overview of lectin-carbohydrate interactions will also be given, together with an insight into their energetics. In addition, therapeutic applications of lectins will be discussed.     

Near-infrared light for polymer re-shaping and re-processing applications

The re-shaping and reprocessing of polymers are usually associated with strong energetic costs, strongly limiting their practical usage. In this article, a new approach is proposed based on a near-infrared (NIR) activation of the material in presence of a NIR heater for a highly efficient process upon ecofriendly NIR light emitting diodes irradiation. Markedly, due to this light-triggered process, a spatial control of the shaping/reprocessing behavior can be obtained, that is, only the needed parts are irradiated preventing a heating of all the sample. In this work, different thermoplastics are reshaped or reprocessed due to NIR activation in presence of an organic NIR dye used as heater. As other examples of photothermal treatment upon NIR light, the on-demand dehydration of polyethylene glycol (PEG-based) hydrogels are also provided. All the processes are followed in real time by thermal imaging camera.     

Oligothiophene isocyanides for platinum-based molecular electronic applications

Understanding molecular orientation on a metal surface is key to designing molecular electronic device junctions. Though platinum device electrodes are of particular interest as a more stable alternative to the often used gold electrodes, the chemisorption of conducting molecules onto platinum surfaces has not been thoroughly studied. We present herein the first detailed study of the ability and manner in which soluble oligothiophene isocyanides, of lengths ranging from 2 to 7 nm, chemisorb onto platinum surfaces and nanoparticles. It was found that these oligothiophene isocyanides stand at a 41 degrees angle from the platinum surface normal, suggesting their applicability in molecule-bridged platinum electrode devices.     

Fluorine conformational effects in organocatalysis: an emerging strategy for molecular design

Molecular design strategies that profit from the intrinsic stereoelectronic and electrostatic effects of fluorinated organic molecules have mainly been restricted to bio-organic chemistry. Indeed, many fluorine conformational effects remain academic curiosities with no immediate application. However, the renaissance of organocatalysis offers the possibility to exploit many of these well-described phenomena for molecular preorganization. In this minireview, we highlight examples of catalyst refinement by introduction of an aliphatic C-F bond which functions as a chemically inert steering group for conformational control.     

Rheological properties of functionalised thermosensitive copolymers for injectable applications in medicine

Functionalised triblock copolymers based on poly((lactic acid)-co-(glycolic acid)) and poly(ethylene glycol) (PLGA-PEG-PLGA) further modified with 3-methylenetetrahydrofuran-2,5-dione (itaconic anhydride; ITA) exhibited sol-gel transition induced by increasing temperature. Rheological properties of a series of ITA/PLGA-PEG-PLGA/ITA copolymer concentrations (6?C24 mass %) in deionised Milli-Q water were studied by both the test tube inverting method (TTIM) and rheometer. The gel stiffness increased with the polymer concentration shifting the gel point of the copolymer to the lower temperature. The present study demonstrates that each method describes a sol-gel transition, but the combined method gives comprehensive information about changes in colour, viscosity, elastic and loss moduli. Characterisation of such a gel is necessary for its further use, in order to determine whether the material is appropriate as an injectable biomedical hydrogel.     

Two-dimensional electrophoresis in small gels for applications in veterinary medicine.

A versatile method for two-dimensional electrophoresis that can be performed easily, even in small routine laboratories, is described. The procedure combines a first-dimensional isoelectric focusing run in a PhastSystem with denaturing electrophoresis in a small vertical electrophoresis chamber. The described arrangement of two first-dimensional gel strips in the second dimension allows direct comparison of two related samples, eliminating most of the artifacts that usually lead to misinterpretations. The presented procedure can be conveniently adapted to the needs of each laboratory; at present, it is being extensively used to establish protein patterns of healthy individuals of different species, a prerequisite with regard to help and support diagnosis.